With two victories in his first two games, and the nation adopting modest expectations for his team at Euro 2012, Roy Hodgson might have thought that he had safely navigated the rockiest period of his first few weeks as England manager. But when Gary Cahill withdrew from the squad yesterday to be replaced by Liverpool's defender Martin Kelly, the most divisive fissure in the group re-opened again.

That is the line that separates Rio Ferdinand from John Terry over the latter's case for allegedly racially abusing Ferdinand's brother Anton and it has the potential to cast a long shadow over this England squad. The decision to ignore Ferdinand's claim on a place in a squad that has already lost the experience of Frank Lampard and Gareth Barry shifted that issue into centre-stage once again.

Yesterday, Kelly was on a flight back from New York where he has been on holiday since he left the England squad a week ago, having been part of the group that travelled to Norway where he played two minutes of the game. Kelly is the innocent party in this but his single cap for England and only 12 league appearances for Liverpool last season contrasts starkly to Ferdinand's 81 caps over 15 years.

Ferdinand is an uncomfortable subject for Hodgson. At his press conference to introduce his squad on 16 May he said that "football reasons" were behind the player not being selected. Hodgson picked seven defenders – which later became eight when Phil Jagielka replaced Barry – and said he took Phil Jones ahead of Ferdinand for his versatility. "I decided on my three centre-backs and Rio wasn't one of them," he said at the time. "There's no point in continuing that discussion. I admire Rio Ferdinand, I respect Rio Ferdinand. But, as a football coach, you have to make decisions sometimes."

It was thin at best but it was just about enough of a foundation for the England manager to bat away the questions asking if Ferdinand's absence was connected to the Terry case. "I can't insult your intelligence and say I wasn't aware of the situation," he said. "Everyone knows a situation has arisen. But I've tried to put it as far from my mind as possible."

By the time Ferdinand tweeted yesterday "What reasons?????!!!" in the aftermath of the decision to call up Kelly in the place of Cahill it was obvious that there must be more to Hodgson's decision than just "football reasons". In private the Football Association maintains that Kelly was with the squad for the first week and they are confident of him coming back in with his fitness levels well-established.

Even when he announced Ferdinand's initial omission, Hodgson did not question the 33-year-old's fitness. As it stands Ferdinand is understood to be in the country and training every day at his gym at home. He is ready to play. Micah Richards, on the other hand, turned down the opportunity to go on stand-by when the squad was selected on the basis that it was Stuart Pearce and not Hodgson who called him with the news.

Whatever the players think about the Ferdinand situation, the usual rules of omerta will be observed. There is a court case pending, after all, but even if there was not, footballers are not given to being outspoken on such delicate topics. At the next England press conference on Thursday in Krakow someone will declare the squad united and attempt to draw a line under it all.

Aside from the politics of the situation, the loss of Cahill is a tough one to take. He was the victim of a cowardly push by Dries Mertens in the 18th minute which sent him headfirst into Joe Hart and a collision that robs the defender of the chance to play at Euro 2012. The Cahill-Terry partnership was well-established and, while Joleon Lescott is a more than adequate replacement, the cover beyond those two is inexperienced.

The defence had threatened to be England's strongest point, especially in the light of an uninspiring win over Belgium at Wembley on Saturday. Much like the one against Norway seven days earlier, it was built on the obduracy of England's defensive work. When it came to the opposition attempts on goal, you could count the chances in both games in the single figures.

They have won both games under Hodgson by single goal. Against Belgium it was a neat finish by Danny Welbeck from Ashley Young's pass for his first international goal. For now, however, the compliment that England are hard to beat is not one that Hodgson wants to accept.

"You're suggesting I have gone in with some major principle and have got the players around and said: 'Now lads, this is what we are going to do, we are going to be hard to beat'," was the England manager's response. "That is not the case at all. When we work on our defending, we work on our defending. When we work on our attacking, we work on our attacking. When we talk to the players about what we are looking for, we talk about both aspects.

"Of course, we do have good defenders... That is what is shining through at the moment. We are very pleased with the work rate from the others. Take James Milner and Steven Gerrard in the last two games, they have done really well. They have taken up good positions defensively. But there is a lot more work for us to do."

Being hard to beat conjures up all sorts of negative connotations that Hodgson rejects. Teams that are hard to beat are grudgingly praised for their stoicism when they are successful – Chelsea in the Champions League this season, Greece at Euro 2004 – but when they fail miserably and go home early, everyone else is delighted. On Theo Walcott, left out for the more conservative Milner, Hodgson was clear that he does not quite trust the Arsenal man enough to pick him.

Suddenly, from nowhere, the Ferdinand issue has been reignited by Cahill's injury. Hodgson will discover that the England manager's job involves fighting fires wherever he can. He just probably did not expect to see this one again so soon.